Total RNA was isolated from cells using RNeasy Mini kit (QIAGEN, #74104) and was treated with DNase I(QIAGEN #79254). Immunoprecipitated DNA purified using QIAquik PCR purification kit (QIAGEN, #28106). RNA-seq libraries were prepared from 2 μg of total RNA, using TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594), according to the manufacturer's instructions. ChIP-seq libraries were prepared from 10 ng of ChIP DNA using the TruSeq ChIP Library Preparation Kit, according to the manufacturer's instructions. Sample preparation for ribosome profiling was conducted according to the manufacturer's specifications for the TruSeq Ribo Profile (Mammalian) Library Prep Kit (Illumina).